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Probably not, because if the user has the settings so that you get an "Active scripting" warning, it would be pretty silly to allow it to be bypassed with what it's blocking (javascript). Also, consider that the user might actually want it this way, and you should never mess with a user's personal preferences.

There is no way to get IE to enable JavaScript as IE doesn't have that ability built in. Instead of allowing for JavaScript, IE instead allows for vbScript and/or jScript (which are the two languages turned on and off by the Active Scripting option). Fortunately jScript can handle most of the same things JavaScript can and for where it can't you can use either feature sensing or conditional comments in the jScript to select whether to run the JavaScript or jScript equivalent code. There are of course lots of things that can be done with jScript and/or vbScript that can't be done with JavaScript (and which are intended for use only on intranets).

The other thing to consider is that activeX is the most buggy security hole ridden piece of software that has ever been created, IE7 now disables most of it by default to plug many of the security holes that it creates but there is no way to plug those hundreds of security holes in IE6 without disabling activeX completely. Doing so then pops up alerts on almost every web page unless you also turn off Active Scripting and so any sensible IE6 user will have Active Scripting disabled simply to get rid of all the annoying activeX error messages..